Managing Plant Resources: How Intensive Can it be?

Previous studies have shown there is a wide spectrum of incipient management practices between gathering and agriculture, that include resources commonly considered “wild.” Based on the study of 20 species used as foodstuffs in the community of Santa María Tecomavaca (Mexico), we evaluated nonagricultural management forms such as gathering, incipient nonselective management, incipient selective management and occasional ex situ cultivation to learn if they represent a gradient in the intensity of manipulation of a resource. The way in which the intensity of manipulation of a resource can vary as a function of cultural importance and the species’ biology was also analyzed. Using an index that measures the intensity of management of a resource, it has been established that the degree of intensity depends on: the specialization of the practices directed to the environment as well as to the individuals; the number of persons performing these practices; and the number of different practices taking place. The degree of management intensity is also a consequence of the joint action of cultural importance and of species’ biology.

Closing Yield Gaps: How Sustainable Can We Be?

Global food production needs to be increased by 60–110% between 2005 and 2050 to meet growing food and feed demand. Intensification and/or expansion of agriculture are the two main options available to meet the growing crop demands. Land conversion to expand cultivated land increases GHG emissions and impacts biodiversity and ecosystem services. Closing yield gaps to attain potential yields may be a viable option to increase the global crop production. Traditional methods of agricultural intensification often have negative externalities. Therefore, there is a need to explore location-specific methods of sustainable agricultural intensification. We identified regions where the achievement of potential crop calorie production on currently cultivated land will meet the present and future food demand based on scenario analyses considering population growth and changes in dietary habits. By closing yield gaps in the current irrigated and rain-fed cultivated land, about 24% and 80% more crop calories can respectively be produced compared to 2000. Most countries will reach food self-sufficiency or improve their current food self-sufficiency levels if potential crop production levels are achieved. As a novel approach, we defined specific input and agricultural management strategies required to achieve the potential production by overcoming biophysical and socioeconomic constraints causing yield gaps. The management strategies include: fertilizers, pesticides, advanced soil management, land improvement, management strategies coping with weather induced yield variability, and improving market accessibility. Finally, we estimated the required fertilizers (N, P₂O₅, and K₂O) to attain the potential yields. Globally, N-fertilizer application needs to increase by 45–73%, P₂O₅-fertilizer by 22–46%, and K₂O-fertilizer by 2–3 times compared to the year 2010 to attain potential crop production. The sustainability of such agricultural intensification largely depends on the way management strategies for closing yield gaps are chosen and implemented.     

Gene Transfer: How Can the Biological Barriers Be Overcome?

Physical methods represent a promising approach for the safe delivery of therapeutic plasmid DNA in genetic and acquired human diseases. However, their development in clinics is limited by their low efficacy. At the cellular level, efficient gene transfer is dependent on several factors including extracellular matrix, plasmid DNA uptake and nucleocytoplasmic transport. We review the main barriers that plasmid DNA encounters from the extracellular environment toward the interior of the cell and the different strategies developed to overcome these biological barriers. Diffusional and metabolic fences of the extracellular matrix and the cytoplasm affect plasmid DNA uptake. These barriers reduce the number of intact plasmids that reach the nucleus. Nuclear uptake of plasmid DNA further requires either an increase of nuclear permeability or an active nuclear transport via the nuclear pore. A better understanding of the cellular and molecular bases of the physical gene-transfer process may provide strategies to overcome those obstacles that highly limit the efficiency and use of gene-delivery methods.     

How Big Is It Really? Assessing the Efficacy of Indirect Estimates of Body Size in Asian Elephants

Information on an organism’s body size is pivotal in understanding its life history and fitness, as well as helping inform conservation measures. However, for many species, particularly large-bodied wild animals, taking accurate body size measurements can be a challenge. Various means to estimate body size have been employed, from more direct methods such as using photogrammetry to obtain height or length measurements, to indirect prediction of weight using other body morphometrics or even the size of dung boli. It is often unclear how accurate these measures are because they cannot be compared to objective measures. Here, we investigate how well existing estimation equations predict the actual body weight of Asian elephants Elephas maximus, using body measurements (height, chest girth, length, foot circumference and neck circumference) taken directly from a large population of semi-captive animals in Myanmar (n = 404). We then define new and better fitting formulas to predict body weight in Myanmar elephants from these readily available measures. We also investigate whether the important parameters height and chest girth can be estimated from photographs (n = 151). Our results show considerable variation in the ability of existing estimation equations to predict weight, and that the equations proposed in this paper predict weight better in almost all circumstances. We also find that measurements from standardised photographs reflect body height and chest girth after applying minor adjustments. Our results have implications for size estimation of large wild animals in the field, as well as for management in captive settings.     

Can Metal Nanoparticles Be a Threat to Microbial Decomposers of Plant Litter in Streams?

The extensive use of nanometal-based products increases the chance of their release into aquatic environments, raising the question whether they can pose a risk to aquatic biota and the associated ecological processes. Aquatic microbes, namely fungi and bacteria, play a key role in forested streams by decomposing plant litter from terrestrial vegetation. Here, we investigated the effects of nanocopper oxide and nanosilver on leaf litter decomposition by aquatic microbes, and the results were compared with the impacts of their ionic precursors. Alder leaves were immersed in a stream of Northwest Portugal to allow microbial colonization before being exposed in microcosms to increased nominal concentrations of nanometals (CuO, 100, 200 and 500 ppm; Ag, 100 and 300 ppm) and ionic metals (Cu²⁺ in CuCl₂, 10, 20 and 30 ppm; Ag⁺ in AgNO₃, 5 and 20 ppm) for 21 days. Results showed that rates of leaf decomposition decreased with exposure to nano- and ionic metals. Nano- and ionic metals inhibited bacterial biomass (from 68.6% to 96.5% of control) more than fungal biomass (from 28.5% to 82.9% of control). The exposure to increased concentrations of nano- and ionic metals decreased fungal sporulation rates from 91.0% to 99.4%. These effects were accompanied by shifts in the structure of fungal and bacterial communities based on DNA fingerprints and fungal spore morphology. The impacts of metal nanoparticles on leaf decomposition by aquatic microbes were less pronounced compared to their ionic forms, despite metal ions were applied at one order of magnitude lower concentrations. Overall, results indicate that the increased release of nanometals to the environment may affect aquatic microbial communities with impacts on organic matter decomposition in streams.     

Fluctuation Analysis: Can Estimates Be Trusted?

The estimation of mutation rates and relative fitnesses in fluctuation analysis is based on the unrealistic hypothesis that the single-cell times to division are exponentially distributed. Using the classical Luria-Delbrück distribution outside its modelling hypotheses induces an important bias on the estimation of the relative fitness. The model is extended here to any division time distribution. Mutant counts follow a generalization of the Luria-Delbrück distribution, which depends on the mean number of mutations, the relative fitness of normal cells compared to mutants, and the division time distribution of mutant cells. Empirical probability generating function techniques yield precise estimates both of the mean number of mutations and the relative fitness of normal cells compared to mutants. In the case where no information is available on the division time distribution, it is shown that the estimation procedure using constant division times yields more reliable results. Numerical results both on observed and simulated data are reported.     

Crop Residue Mass Needed to Maintain Soil Organic Carbon Levels: Can It Be Determined?

Corn’s (Zea mays L.) stover is a potential nonfood, herbaceous bioenergy feedstock. A vital aspect of utilizing stover for bioenergy production is to establish sustainable harvest criteria that avoid exacerbating soil erosion or degrading soil organic carbon (SOC) levels. Our goal is to empirically estimate the minimum residue return rate required to sustain SOC levels at numerous locations and to identify which macroscale factors affect empirical estimates. Minimum residue return rate is conceptually useful, but only if the study is of long enough duration and a relationship between the rate of residue returned and the change in SOC can be measured. About one third of the Corn Stover Regional Partnership team (Team) sites met these criteria with a minimum residue return rate of 3.9?±?2.18 Mg stover ha^?1 yr^?1, n?=?6. Based on the Team and published corn-based data (n?=?35), minimum residue return rate was 6.38?±?2.19 Mg stover ha^?1 yr^?1, while including data from other cropping systems (n?=?49), the rate averaged 5.74?±?2.36 Mg residue ha^?1 yr^?1. In broad general terms, keeping about 6 Mg residue ha^?1 yr^?1 maybe a useful generic rate as a point of discussion; however, these analyses refute that a generic rate represents a universal target on which to base harvest recommendations at a given site. Empirical data are needed to calibrate, validate, and refine process-based models so that valid sustainable harvest rate guidelines are provided to producers, industry, and action agencies.     

The Benefits of Photorespiratory Bypasses: How Can They Work?

Bypassing the photorespiratory pathway is regarded as a way to increase carbon assimilation and, correspondingly, biomass production in C₃ crops. Here, the benefits of three published photorespiratory bypass strategies are systemically explored using a systems-modeling approach. Our analysis shows that full decarboxylation of glycolate during photorespiration would decrease photosynthesis, because a large amount of the released CO₂ escapes back to the atmosphere. Furthermore, we show that photosynthesis can be enhanced by lowering the energy demands of photorespiration and by relocating photorespiratory CO₂ release into the chloroplasts. The conductance of the chloroplast membranes to CO₂ is a key feature determining the benefit of the relocation of photorespiratory CO₂ release. Although our results indicate that the benefit of photorespiratory bypasses can be improved by increasing sedoheptulose bisphosphatase activity and/or increasing the flux through the bypass, the effectiveness of such approaches depends on the complex regulation between photorespiration and other metabolic pathways.In C₃ plants, the first step of photosynthesis is the fixation of CO₂ by ribulose bisphosphate (RuBP). For every molecule of CO₂ fixed, this reaction produces two molecules of a three-carbon acid, i.e., 3-phosphoglycerate (PGA), and is catalyzed by the Rubisco enzyme. A small portion of the carbon in PGA is used for the production of Suc and starch, whereas the remainder (i.e. five-sixths) is used for the regeneration of RuBP (Fig. 1). The regeneration of the Rubisco substrate RuBP in the Calvin-Benson-Bassham (CBB) cycle ensures that ample RuBP is available for carbon fixation (Bassham, 1964; Wood, 1966; Beck and Hopf, 1982). Rubisco is a bifunctional enzyme that catalyzes not only RuBP carboxylation but also RuBP oxygenation (Spreitzer and Salvucci, 2002). RuBP oxygenation generates only one molecule of PGA and one molecule of 2-phosphoglycolate (P-Gly; Ogren, 1984). The photorespiratory pathway converts this P-Gly back to RuBP in order to maintain the CBB cycle.Open in a separate windowFigure 1.Schematic representation of the C3 photosynthesis kinetic model with three different photorespiratory bypass pathways. The bypass described by Kebeish et al. (2007) is indicated in blue, the bypass described by Maier et al. (2012) in pink, and the bypass described by Carvalho et al. (2011) in green. The original photorespiratory pathway is marked in orange, and CO₂ released from photorespiration (including the original pathway and bypass pathways) is indicated in red. 2PGA, 2-Phosphoglyceric acid; ASP, Asp; CIT, citrate; ICIT, isocitrate; PGA, 3-phosphoglycerate; DPGA, glycerate-1,3-bisphosphate; GAP, glyceraldehyde 3-phosphate; DHAP, dihydroxyacetone phosphate; SBP, sedoheptulose-1,7-bisphosphate; S7P, sedoheptulose-7-phosphate; Ri5P, ribose-5-phosphate; Ru5P, ribulose-5-phosphate; FBP, fructose-1,6-bisphosphatase; F6P, fructose 6-phosphate; Xu5P, xylulose-5-phosphate; G6P, glucose-6-phosphate; G1P, glucose-1-phosphate; ADPG, ADP-glucose; F26BP, fructose-2,6-bisphosphate; UDPG, uridine diphosphate glucose; SUCP, sucrose-6F-phosphate; SUC, Suc; PEP, phosphoenolpyruvate; OAA, oxaloacetate; PGCA, phosphoglycolate; GCA, glycolate; GOA, glyoxylate; GCEA, glycerate; MAL, malate; PYR, pyruvate; GLU, glutamate; KG, alfa-ketoglutarate; GLN, Gln; HPR, hydroxypyruvate; RuBP, ribulose bisphosphate; SER, Ser; GLY, Gly; TS, tartronic semialdehyde.In higher plants, P-Gly is dephosphorylated to glycolate, which is transferred into the peroxisomes, where it is oxidized to hydrogen peroxide and glyoxylate. Then, glyoxylate is aminated to produce Gly, which is subsequently transferred to the mitochondria. There, two molecules of Gly are converted into one Ser plus one CO₂ and one NH₃ (Ogren, 1984; Peterhansel et al., 2010). The Ser is ultimately converted back to PGA (Tolbert, 1997). CO₂ and NH₃ are gasses that can escape to the atmosphere (Sharkey, 1988; Kumagai et al., 2011), and the loss of carbon and nitrogen essential for biomass accumulation will decrease the efficiency of photosynthesis and plant growth (Zhu et al., 2010). Fortunately, both substances are partially reassimilated in the chloroplast, but this results in decreased photosynthetic energy efficiency. At 25°C and current atmospheric CO₂ concentrations, approximately 30% of the carbon fixed in C₃ photosynthesis may be lost via photorespiration and the size of this loss increases with temperature (Sharkey, 1988; Zhu et al., 2010). As a result, photorespiration has been regarded as a pathway that could be altered to improve photosynthetic efficiency (Zelitch and Day, 1973; Oliver, 1978; Ogren, 1984; Zhu et al., 2008, 2010).There are several approaches that may be used to alter photorespiration to improve photosynthetic efficiency. First, it might be possible to increase the specificity of Rubisco to CO₂ versus oxygen (S_c/o; Dhingra et al., 2004; Spreitzer et al., 2005; Whitney and Sharwood, 2007). However, previous studies have shown that there is an inverse correlation between S_c/o and the maximum carboxylation rate of Rubisco (Jordan and Ogren, 1983; Zhu et al., 2004), and there are some indications that the S_c/o of different organisms may be close to optimal for their respective environments (Tcherkez et al., 2006; Savir et al., 2010). Second, a CO₂-concentrating mechanism could be engineered into C₃ plants. For example, introducing cyanobacterial bicarbonate transporters (Price et al., 2011) or introducing C₄ metabolism could be used to concentrate CO₂ in the vicinity of Rubisco and, thereby, suppress the oxygenation reaction of Rubisco (Furbank and Hatch, 1987; Mitchell and Sheehy, 2006). Past efforts to introduce a C₄ pathway into C₃ plants have focused on biochemical reactions related to C₄ photosynthesis without taking into account the anatomical differences between C₃ and C₄ plants, which may have been responsible for the limited success of such endeavors (Fukayama et al., 2003). Recently, there has been renewed interest in engineering C₄ photosynthetic pathways into C₃ plants, with efforts focusing on understanding and engineering the genetic regulatory network related to the control of both the anatomical and biochemical properties related to C₄ photosynthesis (Mitchell and Sheehy, 2006; Langdale, 2011).Transgenic approaches have been used to knock down or knock out enzymes in the photorespiratory pathway. Unfortunately, the inhibition of photorespiration by the deletion or down-regulation of enzymes in the photorespiratory pathway resulted in a conditional lethal phenotype (i.e. such plants cannot survive under ambient oxygen and CO₂ concentrations but may be rescued by growing them under low-oxygen or high-CO₂ conditions; for review, see Somerville and Ogren, 1982; Somerville, 2001). Another approach to reduce photorespiration is to block (or inhibit) enzymes in this pathway using chemical inhibitors. Zelitch (1966, 1974, 1979) reported that net photosynthesis increased by inhibiting glycolate oxidase or glycolate synthesis. However, other groups showed that the inhibition of glycolate oxidase or Gly decarboxylation led to the inhibition of photosynthesis (Chollet, 1976; Kumarasinghe et al., 1977; Servaites and Ogren, 1977; Baumann et al., 1981). It turns out that plants cannot efficiently metabolize photorespiratory intermediates without a photorespiratory pathway, and suppression of this pathway inhibits the recycling of carbon back toward RuBP, which is necessary for maintaining the CBB cycle (Peterhansel et al., 2010; Peterhansel and Maurino, 2011). Moreover, the accumulation of toxic metabolic intermediates (e.g. P-Gly) can strongly inhibit photosynthesis (Anderson, 1971; Kelly and Latzko, 1976; Chastain and Ogren, 1989; Campbell and Ogren, 1990). This may explain why earlier attempts to block or reduce photorespiration have failed to improve carbon gain.Instead of reducing photorespiration directly, a promising idea is to engineer a photorespiratory bypass pathway. Such a pathway would metabolize P-Gly produced by RuBP oxygenation but minimize carbon, nitrogen, and energy losses and avoid the accumulation of photorespiratory intermediates. Kebeish et al. (2007) introduced the glycolate catabolic pathway from Escherichia coli into Arabidopsis (Arabidopsis thaliana); we will subsequently call this type of bypass the Kebeish bypass. In such transgenic plants, glycolate is converted to glycerate in the chloroplasts without ammonia release (Fig. 1). Previous studies suggested that this pathway theoretically requires less energy and shifts CO₂ release from mitochondria to chloroplasts (Peterhansel and Maurino, 2011; Peterhansel et al., 2013); experimental results indicated that the bypass allowed for increased net photosynthesis and biomass production in Arabidopsis (Kebeish et al., 2007). There are reports of two other photorespiratory bypass pathways in the literature (Carvalho, 2005; Carvalho et al., 2011; Maier et al., 2012). In the Carvalho bypass (Carvalho, 2005; Carvalho et al., 2011), glyoxylate is converted to hydroxypyruvate in the peroxisome. Similar to the Kebeish bypass, the ammonia release is abolished, one-quarter of the carbon from glycolate is released as CO₂ in the peroxisomes, and three-quarters of the carbon from glycolate is converted back to PGA. However, this pathway has only been partially realized in tobacco (Nicotiana tabacum); that is, the enzyme of the second reaction of this pathway was not detectable in the transgenic plants, and plants expressing this pathway showed stunted growth when grown in ambient air (Carvalho et al., 2011). The Maier bypass (Maier et al., 2012) is characterized by complete oxidation of glycolate in the chloroplasts. Initial results suggested that the photosynthesis and biomass of transgenic Arabidopsis with this pathway were enhanced (Maier et al., 2012).Recently, the design and benefits of the three bypass pathways were reviewed (Peterhansel et al., 2013), and it was suggested that a photorespiratory bypass can contribute to an enhanced photosynthetic CO₂ uptake rate by lowering energy costs and minimizing carbon and nitrogen losses. However, a systematic and quantitative analysis of the potential contributions of these different factors to photosynthesis improvement has not yet been conducted. Systems modeling can help to design new metabolic pathways and improve our understanding of biochemical mechanisms (McNeil et al., 2000; Wendisch, 2005; Zhu et al., 2007; Bar-Even et al., 2010; Basler et al., 2012). Such models have been used successfully to gain insight into the photosynthetic metabolism (Laisk et al., 1989, 2006; Laisk and Edwards, 2000; Zhu et al., 2007, 2013; Wang et al., 2014). In this study, we use an extended kinetic model of C₃ photosynthesis based on earlier work by Zhu et al. (2007) to systematically analyze the potential of three photorespiratory bypass pathways for improving photosynthetic efficiency (Supplemental Model S1). In addition, we determined under what conditions such bypass pathways may lead to increased photosynthesis and biomass production in C₃ plants and how to further improve the photosynthesis of plants with such a bypass. Our analysis suggests that the benefit of a photorespiratory bypass varies dramatically if it is engineered into different crops.     

Can Eph Receptors Stimulate the Mind?

The Eph receptors are multitalented tyrosine kinases capable of performing many tasks. The receptors together with their ligands--the ephrins--are well known to play a critical role in the initial assembly of neuronal circuits in the embryo. However, the recently discovered function of these receptors in the adult brain is now receiving significant acclaim. Three new articles show that the Eph receptors continue to be important in modifying the strength of existing neuronal connections (synapses). They do so in close association with at least one family of ion channels, the NMDA receptors.     

How Fast Can Carbon Be Sequestered When Restoring Degraded Subtropical Thicket?

Is the maximum rate of carbon sequestration reported for the CAM‐C₃ plant Portulacaria afra (spekboom), viz. 15.4 t CO₂ ha^?1 yr^?1, unusual in comparison with other plants with similar physioliogies, or could such rates be expected routinely in restoration with P. afra? Private sector investors in thicket restoration need an answer to this question in order to assess the feasibility of using carbon finance as the main income stream from their investments. A literature review showed that 15.4 t CO₂ ha^?1 yr^?1 is not an unusual rate of carbon sequestration for CAM plants in arid and semi‐arid environments, which suggests that investors in thicket restoration should not consider this an outlier value. The results also suggest that carbon finance could be used to fund restoration using other CAM plants in degraded xeric thickets in countries such as Argentina, Chile, Mexico, and Madagascar.